Box 12 from my W2 is not pulling over to reflect my employer/payroll contributions. Why can I not manually fill this out? My HSA is not showing up otherwise. What to do?

Any HSA contributions in box 12 were already subtracted from your box 1 taxable wages, so you already got the tax benefit by having lower income, therefore lower taxes.  If you think your employer has not reduced your box 1 taxable wages, you need to discuss with your employer to get clarification and possibly a corrected W-2. 

To clarify: does your W-2, Box 12 include a Code W, which shows total contributions made to a Health Savings Account (HSA)? This includes employer contributions and employee payroll deductions.

If your W-2 has Code W in Box 12, that amount should automatically transfer to the correct HSA contribution area in TurboTax.

You would not want to enter information on a W-2 that is not on the original form because it will cause a mismatch with the IRS. If you think that your employer mistakenly left the HSA contributions off of your W-2, you should request a corrected W-2.

HSA contributions made via payroll are pre-tax, so they are not included in your W-2's Box 1 (wages) and are not included in income on your tax return. 

Any HSA contributions you made on your own (after-tax) are deducted on your tax return on Schedule 1, Line 13 as an adjustment to income.

Here is a TurboTax article on HSA's for more information.

in addition, HSA contributions made through your employer should show up on line 9 of Form 8889